The biggest twist of the episode is the death of Fitz and Mellie's son, Jerry. He dies after getting infected with a substrain of bacterial meningitis, which is available only at Fort Detrick. Fitz is sure that Mom Pope has killed his son and he asks Pop Pope, Rowan, to take her down at any cost.
B-613 is back in business and Rowan's gets back his B-613 crown. He tells Fitz that Mom Pope has been eliminated. In reality, he has kept her in an underground dungeon.
Fitz was all set to lose the election to Sally, but the death of his son gives him another four years in the White House. At the end of the episode, Fitz breaks down. He is not the re-elected President but a broken father who has lost his son.
Olivia feels that she needs to be fixed, as whatever bad is happening is because of her. "I'm the thing that needs to be fixed, I'm the thing that needs to be handled. I'm the Scandal," she says in the season finale of "Scandal." She takes up her father's offer, which she had refused in the first episode of season three, to get on a plane and get out of the mess. Jake gets on that plane, as well, so that he can stand in the sun with Olivia. In one of the scenes, Olivia confesses that she loves Fitz and feels guilty that she felt something when she had sex with Jake.
Harrison figures out that it is Rowan who had planned out the killing of Jerry. When he accuses Rowan of planning the whole thing, the reinstated command of B-613 does not deny that. He has his twisted logic to offer.
It is Tom, one of B-613 agents, who had infected Jerry with bacterial meningitis on Rowan's orders. According to Rowan, the death of Jerry ensured that Fitz won the election, as her daughter wanted him to win. He also kept his promise to Olivia that he would not harm a hair of Fitz's head. Rowan adds, "He took my child, so I took his."
Tom points a gun at Harrison, but it is not shown whether he kills him.
Fitz and Mellie are unable to get in touch with Olivia, as she ignores their phone calls. She is flying off to an undisclosed location, with Jake sitting beside her. Also, the episode features a moment when Fitz comes to know from Olivia that Mellie was raped by his father.